AMBER Archive (2006)

Subject: Re: AMBER: running sander on several nodes

From: Fenghui Fan (fenghui_fan_at_yahoo.com)
Date: Thu Sep 28 2006 - 12:21:26 CDT

Dear all,

I input the following command:
 mpirun -np 4 $AMBERHOME/exe/sander -ng 2 -groupfile
<$AMBERHOME/exe/sander -O -i md25000ps.in -o
md25000ps.out -p epac1modeller.prmtop -c md1.rst -r
md25000_md2.rst -x md25000ps_md2.mdcrd>

and I got the following message:
Missing name for redirect.

Will you please tell what is wrong with my input?

I am looking forward to getting your message.

Best regards.

Fenghui Fan

--- Fenghui Fan <fenghui_fan_at_yahoo.com> wrote:

> Dear all,
>
> I have a cluster with AMBER installed. When I run
> amber, I am not allowed to use MAster node. As I
> know,
> runnning Sander in several nodes for a single
> ruuning
> is allowable.
>
> Will you please tell me the commands to run sander
> in
> several nodes so that I can shorten the time for
> calculation? At this moment those who are
> responsible
> for he cluster do not know this commands.
>
> I am looking forward to getting your message.
>
> Best regards.
>
> Fenghui Fan
>
>
>
>
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